data_1KWO # _model_server_result.job_id CfvO0RBj2aF0FoHdqtC3PQ _model_server_result.datetime_utc '2025-01-10 12:03:46' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 1kwo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":999}' # _entry.id 1KWO # _exptl.entry_id 1KWO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 95.16 _cell.angle_beta 96.45 _cell.angle_gamma 100.93 _cell.entry_id 1KWO _cell.length_a 51.816 _cell.length_b 57.028 _cell.length_c 151.708 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KWO _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A SG CYS 693 A CYS 693 1_555 F CP9 PDM . A PDM 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? covale ? covale2 A NZ LYS 705 A LYS 705 1_555 F C13 PDM . A PDM 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.366 ? metalc ? metalc1 A OG1 THR 183 A THR 183 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc2 A OG SER 241 A SER 241 1_555 D MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 D MG MG . A MG 903 1_555 E O2G AGS . A AGS 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc4 D MG MG . A MG 903 1_555 E O1B AGS . A AGS 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 B O ASP 28 B ASP 28 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc6 B OD1 ASP 28 B ASP 28 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.722 ? metalc ? metalc7 B OD2 ASP 30 B ASP 30 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc8 B N ARG 31 B ARG 31 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc9 B OD1 ASP 32 B ASP 32 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc10 B N ASP 32 B ASP 32 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc11 B O PHE 34 B PHE 34 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc12 B OD1 ASP 39 B ASP 39 1_555 H MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc13 C O ASP 19 C ASP 19 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc14 C OD1 ASP 19 C ASP 19 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc15 C O ASP 22 C ASP 22 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc16 C OD1 ASP 22 C ASP 22 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc17 C O GLY 23 C GLY 23 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc18 C OD2 ASP 25 C ASP 25 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc19 C O ALA 27 C ALA 27 1_555 G CA CA . C CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc20 G CA CA . C CA 501 1_555 K O HOH . C HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 1KWO _atom_sites.fract_transf_matrix[1][1] 0.019299 _atom_sites.fract_transf_matrix[1][2] 0.003725 _atom_sites.fract_transf_matrix[1][3] 0.002624 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017859 _atom_sites.fract_transf_matrix[2][3] 0.002049 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006677 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 MG A 1 903 503 MG MG . E 5 AGS A 1 999 999 AGS ATP . F 6 PDM A 1 900 693 PDM CYP . G 7 CA C 1 501 501 CA CA . H 4 MG C 1 902 502 MG MG . I 8 HOH A 1 1000 3 HOH WAT . I 8 HOH A 2 1001 4 HOH WAT . I 8 HOH A 3 1002 5 HOH WAT . J 8 HOH B 1 157 1 HOH WAT . K 8 HOH C 1 903 2 HOH WAT . K 8 HOH C 2 904 6 HOH WAT . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PG AGS . . . E 5 12.366 4.568 -26.871 1 105.61 ? PG AGS 999 A 1 HETATM 2 S S1G AGS . . . E 5 10.541 4.12 -27.564 1 98.63 ? S1G AGS 999 A 1 HETATM 3 O O2G AGS . . . E 5 13.448 3.976 -27.89 1 97.69 ? O2G AGS 999 A 1 HETATM 4 O O3G AGS . . . E 5 12.492 4.001 -25.478 1 97.37 ? O3G AGS 999 A 1 HETATM 5 P PB AGS . . . E 5 13.615 7.219 -26.618 1 66.11 ? PB AGS 999 A 1 HETATM 6 O O1B AGS . . . E 5 14.787 6.847 -27.387 1 51.08 ? O1B AGS 999 A 1 HETATM 7 O O2B AGS . . . E 5 13.742 7.327 -25.174 1 71.99 ? O2B AGS 999 A 1 HETATM 8 O O3B AGS . . . E 5 12.419 6.18 -26.981 1 75.13 ? O3B AGS 999 A 1 HETATM 9 P PA AGS . . . E 5 13.704 9.669 -28.128 1 22.42 ? PA AGS 999 A 1 HETATM 10 O O1A AGS . . . E 5 15.003 9.999 -27.514 1 56.08 ? O1A AGS 999 A 1 HETATM 11 O O2A AGS . . . E 5 13.644 9.378 -29.58 1 45.55 ? O2A AGS 999 A 1 HETATM 12 O O3A AGS . . . E 5 13.094 8.508 -27.264 1 27.9 ? O3A AGS 999 A 1 HETATM 13 O O5' AGS . . . E 5 12.798 10.772 -27.8 1 33.71 ? O5' AGS 999 A 1 HETATM 14 C C5' AGS . . . E 5 11.753 11.067 -28.456 1 59.58 ? C5' AGS 999 A 1 HETATM 15 C C4' AGS . . . E 5 11.68 12.554 -28.569 1 43.71 ? C4' AGS 999 A 1 HETATM 16 O O4' AGS . . . E 5 11.386 13.418 -27.426 1 34.97 ? O4' AGS 999 A 1 HETATM 17 C C3' AGS . . . E 5 12.864 13.185 -29.26 1 44.52 ? C3' AGS 999 A 1 HETATM 18 O O3' AGS . . . E 5 12.812 12.796 -30.645 1 44.06 ? O3' AGS 999 A 1 HETATM 19 C C2' AGS . . . E 5 12.606 14.632 -29.005 1 52.49 ? C2' AGS 999 A 1 HETATM 20 O O2' AGS . . . E 5 11.679 15.223 -29.917 1 29.34 ? O2' AGS 999 A 1 HETATM 21 C C1' AGS . . . E 5 12.055 14.693 -27.568 1 52.03 ? C1' AGS 999 A 1 HETATM 22 N N9 AGS . . . E 5 13.13 14.844 -26.51 1 76.21 ? N9 AGS 999 A 1 HETATM 23 C C8 AGS . . . E 5 13.679 13.89 -25.693 1 84.39 ? C8 AGS 999 A 1 HETATM 24 N N7 AGS . . . E 5 14.624 14.313 -24.887 1 77.88 ? N7 AGS 999 A 1 HETATM 25 C C5 AGS . . . E 5 14.667 15.664 -25.168 1 66.9 ? C5 AGS 999 A 1 HETATM 26 C C6 AGS . . . E 5 15.536 16.703 -24.714 1 51.92 ? C6 AGS 999 A 1 HETATM 27 N N6 AGS . . . E 5 16.395 16.476 -23.741 1 49.63 ? N6 AGS 999 A 1 HETATM 28 N N1 AGS . . . E 5 15.36 17.954 -25.207 1 56.99 ? N1 AGS 999 A 1 HETATM 29 C C2 AGS . . . E 5 14.483 18.161 -26.189 1 58.31 ? C2 AGS 999 A 1 HETATM 30 N N3 AGS . . . E 5 13.637 17.283 -26.724 1 76.5 ? N3 AGS 999 A 1 HETATM 31 C C4 AGS . . . E 5 13.843 16.001 -26.22 1 78.04 ? C4 AGS 999 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #